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2026-03-22 19:55:49 +00:00
parent 3560dfd611
commit c95646d39c
120 changed files with 617 additions and 675 deletions
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reference/count.md
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@@ -188,17 +188,15 @@ calculate microbial resistance and susceptibility.
# base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R"
#> ℹ `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline
#> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ `?count_resistant()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options.
#> ℹ This message will be shown once per session.
#> [1] 804
count_susceptible(example_isolates$AMX) # counts "S" and "I"
#> ℹ `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST
#> guideline and thus considers the 'I' category susceptible. Set the
#> `guideline` argument or the `AMR_guideline` option to either "CLSI" or
#> "EUCAST", see AMR-options (`?AMR::AMR-options`).
#> ℹ `?count_susceptible()` assumes the EUCAST guideline and thus considers the
#> 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options.
#> ℹ This message will be shown once per session.
#> [1] 546
count_all(example_isolates$AMX) # counts "S", "I" and "R"
@@ -229,10 +227,9 @@ n_sir(example_isolates$AMX)
count_susceptible(example_isolates$AMX)
#> [1] 546
susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
#> ℹ `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline
#> and thus considers the 'I' category susceptible. Set the `guideline` argument
#> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options
#> (`?AMR::AMR-options`).
#> ℹ `?susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see AMR-options.
#> ℹ This message will be shown once per session.
#> [1] 546
@@ -279,8 +276,8 @@ if (require("dplyr")) {
group_by(ward) %>%
count_df(translate = FALSE)
}
#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB' (tobramycin),
#> 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For `?aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin),
#> AMK (amikacin), and KAN (kanamycin)
#> # A tibble: 12 × 4
#> ward antibiotic interpretation value
#> <chr> <chr> <ord> <int>